NCIS Case File: Avengers Assemble
by FantasyWriter93
Summary: Summary inside, as well as possible pairings. WARNING: This has slash ManXMan and Het ManXWoman pairings, if this offends you do not read. No flames please.
1. Prologue

_**NCIS Case File: Avengers Assemble**_

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**Category:** NCIS/Avengers

**Rated:** M (NC17) – Slash, Lemons, Violence, Blood

**Pairings: **

Gibbs/ Tony **or **Tony/Steve R. (Captain America) **or** Gibbs/Tony/Steve R.

Phil Coulson/Clint Barton

? McGee/Thor?

? Abby/Bruce?

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**Summary: **

His life has always been watched it seems, or maybe it was just when Tony started to have strange powers begin to develop. One case with NCIS that might have killed them all has compromised his secrets, at least to that of SHIELD's eyes and ears. With Loki threatening to destroy the world and Director Fury is as desperate as he seems, Tony is asked to come in. But with this new case, Gibbs and the team begin to ask questions that Tony cannot and will not answer, even if it means losing the ones he loves. However, Gibbs has connected the dots and goes in after him, leading the rest of the team along with him.

_"This is nothing you have ever fought against Gibbs. You are fighting against things you cannot begin to believe and this time, I don't think that Marine luck of yours will hold out.__"_

**I do not own NCIS or the Avengers, because if I did, they would have slash pairings all the way!**

**ENJOY!**

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**~*~*~ NCIS Case File: Avengers Assemble - Prologue ~*~*~**

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"Anthony, time for bed," the woman called as she sat down on the bed that belonged to her five year old son.

"Coming mother!" was hollered from the nearby bathroom, if a bit muffled.

She chuckled as the gurgle that followed and the rush of a tap being turned on. She looked to her left to see the box that she had placed on the bed still beside her.

The pitter-patter of small feet on wood grew louder as the small boy ran towards the bed before laughing and jumping the bed, snuggling under the covers as he looked up at his mother.

Lady Dinozzo chuckled at the boy, tucking the sheets further around him, keeping him warm in the winter night.

"All tucked in tight?" she whispered.

Anthony giggled before nodding at his mother.

"Now about that story I was going to tell you?" she hummed, acting like she had forgotten as she tapped her chin, "What was I going to tell you again?"

Anthony giggled again, though softer as he tried to hide behind his hands, "You were going to tell me about the family he-hearbloum,"

"Close Tonio, the family heirloom," she stated, before picking up the box next to her and placing it on her lap.

"Now where was I. Oh yes, a long time ago, when the gods still lived among the mortals and magic protected its people, a magic cube of energy fell from the heavens,"

The little boy smiled as the images began to appear in his imagination.

"This cube was so small to the gods and so ordinary to the mortals that none thought to think about what it could mean. One day, the energy from the cube began to help the plants grow and the people began to grow stronger as well as they were in its presence, but those who dared to touch the cube were never seen again,"

Small eyes grew wide at her words.

"Men began to fight amongst themselves for the power of the cube, the cube drawing on their anger and making it stronger. Unfortunately for the people, war broke out over the cube,"

She took a deep breath before grabbing the child's small hand reassuringly.

"The gods, seeing man's war, took the cube from man and hid it away on their realm. Both to protect it from man and that of the worlds that may come for its power,"

Anthony titled his head in confusion, "But what does this have do with the family heirloom mommy?"

"Patience, little one, patience," she chuckled, "Can I continue?"

The little boy nodded.

"Well now. Before the gods took it, one brave man attacked the cube, hoping to destroy and bring peace back the world of Man. But it was too strong and the blast took his life. However, one slither of the cube broke off and fell into a nearby river, only to be swept off by the water. No one ever noticed the missing piece before the cube was taken away," she finished softly.

She opened the box on her lap to reveal a beautiful blue crystal and glowed softly on the padded surface it resided on. Pulling the necklace attached, she unlatched so she could hang the chain around her son's neck, letting the crystal fall until it resided upon his chest.

"My mother always told me this story and told me that this crystal was supposedly the lost slither of the magic cube. She told me it would protect me and give me luck in my life. Now I'm giving it to you," she finished kissing her son's forehead softly and tucking him back into the covers.

"Thanks for the story mommy. I will take real good care of the necklace," the little boy said, yawning softly.

"I'm sure you will Anthony. Good night," she said, turning off his light.

"Night mommy," Anthony whispered before falling asleep.

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**~*~*~ NCIS Case File: Avengers Assemble ~*~*~**

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Tears fell down the ten year olds face as he looked upon the photo of his now dead mother on his nightstand.

Tony Dinozzo sniffed before wiping the tears from his face. He shivered at the look on his father's face when he had sneered down on him, the old man's thoughts screaming at him, blaming him for his mother's death.

'_I'm only ten, what more could I have done to save her than he could?_' he thought bitterly of the old man.

His bitter emerald eyes fell down to the crystal on his chest, picking it up and holding it in his hand.

"So much for bring my life luck, all I want is my mother back," he whispered harshly, throwing the crystal against the wall.

It tinkled softly as it fell to the floor. Tony looked back over the small crystal, the only reminded of his mother he had left.

He slowly rose to his feet and kneeled down to grab the crystal. He sighed and stood, walking over to the small safe that he had kept hidden from his father.

He placed the crystal inside, stopping to look at it for a moment. His mind and thoughts were now his own, as it should be.

"I will never put it back on, it has only brought me heartache and confusion. It shall stay in the dark," Tony whispered.

The door of the safe closed leaving the crystal to glow in the darkness.

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**Please read and review, I want to know what you think of this new idea of mine. (EVEN THOUGH I SHOULD BE FINISHING MY OTHER STORIES XD)**

**Also let me know on what you think for the main pairing with Tony. A, B or C?**

**JA NE!**


	2. Chapter 1

**I do not own NCIS or the "Avengers", or associated characters. They are merely toys to play with in this little dollhouse I call a plot. XP**

**Hmm, I'm still toying with the idea of Gibbs/Tony/Steve pairing but I seem to be heading towards a Tony/Steve pairing. Check out the poll on my profile page to cast your vote on the pairing. This will be taken into account for my end decision. **

**ENJOY!**

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**~*~*~ NCIS Case File: Avengers Assemble - Chapter 1 ~*~*~**

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Silence echoed through the hollow construction floor as the stand of between drug gang and NCIS team ensued. Four heavily armed me from a drug-selling gang associated with the death/murder of the wife of an American Naval Petty Officer.

The same Petty Officer who was now standing opposite Gibbs with a vicious smirk on his face.

"You can still give up and come away quietly. No one needs to get hurt," Gibbs stated, trying to hold his anger in.

The leader, Daniels, sneered at him, before it turned into a toothy smirk like that of a shark's grin. The change shook the team; they all began to think the same thing.

'_That can't be good!_'

"I don't think you understand how serious we are. Let me show you," Daniels said.

A hang gun was drawn so quickly from behind his back that they barely had enough time to dive for cover.

**Bang** rang repeatedly through the air followed by cries of pain from the members of the team as they dove behind cement pillars.

Tony turned to see Gibbs clutching at his right bicep, gritting his teeth in pain. It was a through-and-through shot.

Tony pulled off his tie and grabbed Gibbs' arm. Gibbs' eyes glared at him.

"Suck it up boss, I've got to at least try and stop the major bleeding or that will be the only reason you don't survive this," Tony growled at the man.

With a sigh and a nod, Gibbs raised his arm for Tony who tied the strip of material, compressing the wound to stop the flow of blood.

A groan could be heard from McGee, Tony turned in time to see Ziva looking at the bullet graze on McGee's arm.

McGee groaned as he pressed a hand to the graze, "Can't believe we fell for that assholes lies,"

"He played us all," Ziva replied, "He had us from the start,"

Tony looked down as he felt his mask slowly fall off his, the disappointment and shame piling in his stomach. He should have listened to his guts and the distant thrum in the corner of his mind that had sensed an aura of danger from the Petty Officer.

'_I should have felt this long ago. I should have known that he was bad news. I could have stopped us from being shot at and then being almost killed. I could have prevented this showdown. It's all my fault,_' he thought.

Tony groaned as a pounding headache began to brim to the surface of his mind. This was not the time for him to worry about the small but effective barrier around the far corner of his mind. The same one that he held since he took off his mother's heirloom as a child for the first time. The one he had placed around the energy that used to radiate through his body and the once seemingly innocent powers he had tried to control.

The same powers that should have been able to prevent the death of his mother.

The same powers that were now leaking through his slowly cracking barriers.

Shaken from his thoughts, he turned back to the matter at hand.

The man who the Petty Officer had sided with began to laugh, "Last chance to give up Gibbs, make it easy on yourselves and we will make your deaths as painless as possible,"

"Bullshit," McGee groaned softly from the other pillar. Ziva chuckled at his misplaced humour.

"No way in hell! If we are to go down, then we are taking you bastards with us," Gibbs growled, almost looking around the pillar at the leader.

'Not if I have any say about this!' Tony thought as he pushed more at the small cracking barrier in his mind.

As the cracks in the barrier began to break into a great web of cracks, Tony smirked as his emerald eyes began to show a blue tinge to anyone who could see his eyes at that moment.

|| **Rule Sixteen: If someone thinks they the upper hand . . . BREAK IT!** || Tony thought as a wave of telepathic energy swept from his mind towards the minds of the enemy.

Tony's eyelids dropped as he was swept into river of thoughts, emotions and memories from the four men on the otherwise of the floor of the half-constructed building. His eyes flickered behind his eyelids as his mind began to sweep through the flood of information that he had to process, looking for any sign or chance that he could use against the men to try and get the upper hand on the drug gang.

His blue tinged eyes shots open in shock from the images that he was receiving from the detected Petty Officer. The blue began to fade away from his emerald eyes as the energy returned to the corner of his mind.

The information he had gained from the man could give them the edge and advantage to take down the enemy without casualties . . . or at least he hoped so.

|| **Rule Thirty-Six: If you think you're being played, you probably are** ||

"I wouldn't do that just yet if I were your Daniels, especially when I know something about our dear Petty Officer that you should probably know," Tony called out from the pillar.

The team looked at him and gaped, "What the hell are you going on about Dinozzo?" Ziva snarled.

Tony ignored her as he could almost literally hear the gears turning in the gang leader, Daniels, head turning.

It was clear to Tony that Daniels was doubting the Petty Officer as well from the clear hesitance and reluctance in the mans voice, "I'm listening,"

'_GOTCHA!_' Tony thought.

"Can I at least come out to talk to you face to face without being shot at?" Tony proposed.

Gibbs hissed at him angrily drawing Tony's attention to his boss, "What the hell are you doing?"

"Trying to save our asses without being shot at Boss! I have to try something," Tony snarled back at the man, but only loud enough for the greying many to hear.

Gibbs began to speak again but was interrupted by Daniels reply.

Said man nodded to himself, "Roll out your gun and I will let you talk,"

The Petty Officer cried out angrily at Daniels, "Are you insane? Don't listen to him, just shoot the bastard!"

"Shut up Roberts!" Daniels shouted, punching the man in the guts.

Roberts grunted as he clutched at his stomach, winded from the punch. The glare that he sent the man was ignored by the gang leader.

Tony ignored the confrontation between the two as he pulled his gun from the holder inside his jacket and pushed it away from the pillar. He turned to walk out from behind the pillar only to be stopped by the whack on the back of his head that he received. He turned to see the cold blue gaze of Gibbs looking at him.

"If I wasn't in pain right now I would shoot you myself," Gibbs growled.

Tony rolled his eyes, "Rule 16 Boss, you should try listening to your own rules more often," he stated as he stepped out from behind the pillar with his hands in the air with his jacket open showing his empty gun holster.

Tony looked out to see Daniels sneering at him with his gun still raised and directed at him.

"Now what was it you wanted to say Cop?" Daniels asked.

"You are being played by Roberts," Tony monotoned.

Roberts stiffened at the accusation and his face almost paled.

"How so?" Daniels asked glancing at his accomplice.

"Your getaway car has 3 kilos of C4 hidden under the carriage ready to blow by just a twitch of his fingers - the switch is in his pocket," Tony explained.

Shock reigned through the drug-gang at the revelation, they turned their angry gazes upon the Petty Officer. The man in question was pale and sweaty, practically giving away the truth to the men.

"Why the hell are you believing him? He's a cop! He's trying to distract you," Roberts tried in a last desperate attempt.

Tony groaned as the whirlwind of emotions pulsing around him were pushing harshly at the barriers that he had tried to erect around his abilities in a desperate attempt to control the, and hold them at bay. The barrier itself was cracking further in the spider web of pieces, more energy seemed to leek through the cracks. Tony shook his head to break himself away from the energy and bring him back to reality.

The men were all still glaring angrily at Roberts who shook with nerves. The man was a brilliant actor but not good when it was his life on the line.

"Check his pocket if you don't believe me," Tony stated in a last pitch attempt.

With a nod from Daniels, the other crones grabbed Roberts' arms holding him as the man himself had tried to bolt from them, only to fail. Daniels strode forward and searched Roberts' pockets till he found a detonator in Roberts' side pocket.

Daniels glared in anger at the traitor, "We should have killed you instead of your wife. Don't worry, I'll soon fix that mistake.

Tony gasped as he felt the push in his mind as to Daniels intentions. Without thought for his own safety Tony leapt forward just in time to push the leader away from the man who was would have been his stabbing victim.

But the thug who had been holding the detonator twitched from the shock of Tony's attack that he hit the switch.

The explosion rocked the building as the following shockwave of exploding car swept through the supports causing it to almost waver and shake from the cascading force of fire and metal.

Tony rolled along the floor with heavy weight of Daniels rolling on top of him. The man punched him in the head but the blow was pushed off centre as Tony bucked up and rolled the man over to be underneath him. The two continued that way as they continued roll further away from the original scene and further into the construction. Their groans and grunts of pain echoing along the floor.

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**~*~*~ NCIS Case File: Avengers Assemble ~*~*~**

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Gibbs shook his head and stood up in a rush to knock the three men out and handcuff them. Ziva and McGee leapt after him, following to cuff the other two men as they lay stunned by the blast.

Gibbs sighed and relief as he saw the three handcuffed men.

"Wait! Where is the fourth - Daniels?" Gibbs asked.

Ziva looked around to before gasping, "Tony!

Gibbs looked over to where Ziva was pointing and ran towards the two tumbling men, "TONY!" he shouted as he watched the Tony and Daniels rolled over of the uncompleted elevator shaft.

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**~*~*~ NCIS Case File: Avengers Assemble ~*~*~**

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In the din of the brawl, Tony heard shouts of his name as the ground beneath him and Daniels fell away. They cried out in shock, breaking from their hold on each other as they continued to fall, the darkness of the drop closing in on them.

'_NO!_' Tony thought as the dam around his powers shattered completely.

A blue aura shaped his body before a large pulse pushed him away the elevator shaft to a floor that was still being constructed.

Tony grunted as he rolled on the floor before skidding to a stop, the dust settling around him and on his clothes.

He coughed the dust from his lungs, moaning at the pain that began to make itself known to his nerves. With one last push of energy, he stood up. His vision blacked out in spots before he shook his head and made unsteady steps towards the empty shaft. Tony looked down.

He could just barely see the broken body of the drug-gang leader. Daniels head was bent at an awkward angle, he could have only snapped his neck.

Ringing echoed in his ears as he fell away from the edge and darkness descended upon him. Tony had reached unconsciousness as shouts rang through the half-formed halls.

"TONY!"

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**~*~*~ NCIS Case File: Avengers Assemble ~*~*~**

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White light appeared before his eyes as Tony blinked into consciousness. He hissed in pain from the pounding that was echoing in his head from the light as struggled to sit up. Bringing a hand to his head, he closed his eyes just in time to hear as the swish of automatic doors opening from his surroundings

"Well my dear boy, I must say that you gave us all a grave scare today, that could have been you found on the bottom of that elevator shaft and not the poor fellow who is sitting on my other autopsy table,"

Tony looked up to see Ducky walking towards him in his green scrubs. Ducky had a smile on his face though his eyes looked red from crying as the emotions that echoed from the man spoke of grief, hope and happiness.

He turned to look over at the next autopsy table to see a black body bag on top with the face zipped open to reveal the open eyes of Daniels. Tony turned away from the body as his stomach began to twist badly at the sight. That could have been him.

"Just lucky I guess," Tony whispered morbidly.

Ducky nodded in understanding, "Well my boy, you have only a few bruises from your fight and from falling back on the floor from the shaft. How are you feeling on a scale of 1 to 10 and don't you dare exaggerate anything less from the truth?"

Tony chuckled from the look of knowing and the glare he received, "About a 6 doc, my head feels like a bongo drum is playing and my muscles are starting to ache a little,"

"Not to worry, nothing a few painkillers can't cure," Ducky stated as he pulled a bottle of aspirin from his pocket.

"Thanks Duck," Tony said taking the bottle and jumping off the table.

Ducky nodded at his back as Tony exited Autopsy. Tony slumped backwards against the elevator wall as the doors closed behind him.

Hitting the emergency switch, Tony took a moment to take everything in.

'_Gods, after so long, I finally use my powers and another man is dead because I couldn't control them. Fuck my life, these powers are either a gift or curse and I still fucking decide which,_' Tony thought with a sigh.

Silence reigned the box as his mind blanked for a moment, just listening to the soft whispers of the thoughts that were being broadcasted from the many workers of NCIS. He '_Shit! Gibbs is going to kill me! Not to mention question my every move from now one, damn I just had to use the blasted things!_' Tony thought as he started the elevator up again and rose towards the floor of the bullpen.

The doors opened to the dark and almost empty bullpen. Ziva and McGee were typing away at their reports but sometime glancing up at different times to his desk with worried glances.

"Aw Probies do you really worry about me that much?" Tony laughed as he strode forward, "I'm touched that you care for me so much,"

"Tony!" the two shouted before rushing up to him.

Ziva leapt into his arms while McGee slapped him on the back.

Ziva let go off him to punch him in the shoulder, swearing in Arabic, "You stupid, stupid man! You could have been killed!"

"But I wasn't and none of us were killed, which I think is a really good thing to the alternative. Personally , I think it's about time that Karma gave me some good luck for once and especially at this time," Tony stated as he sat down at his desk and downed a couple of painkillers.

Ziva went back to her desk and sat down, McGee however continued to stand, "How the hell did you do to survive the fall like that?"

Tony stumbled for a few seconds trying to come up, "I don't really know, I think I blacked out for a few moments and found myself lying on the floor and in the dust. Like I said, just lucky,"

Ziva and McGee looked at him with disbelief in their eyes, but they knew not push him until they really needed too but the suspicion would always remain.

The doors to MTAC opened and Gibbs exited before walking down the stairs, he spotted Tony and the same suspicious gaze looked down on him.

|| **Rule Thirty-Nine: There is no such thing as coincidence** || Tony thought as his boss reached the bottom of the stairs but headed towards the elevator in need of his regular coffee.

Tony shivered at the emotions of mistrust that echoed from all three members of his team, '_I don't think my secret will be my own for much longer. Gods helps me when that happens,_'

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**~*~*~ NCIS Case File: Avengers Assemble ~*~*~**

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"There's a lot we'll have to bring you up to speed on if you're in," Fury explained, his one eye locked onto the blue ones of the American Army Captain from the 1940's, "The world has gotten even stranger than you already know,"

Captain Steve Rogers shook his head softly at the man, "At this point, I doubt anything would surprise me,"

"Ten bucks says your wrong," Fury said as he watched the other man gather up his gear, "There is a debriefing package waiting for you at your apartment,"

Steve just continued to walk away, almost ignoring his superior officer.

"Is there anything you can tell us about the Tesseract that we ought to know now?" Fury asked.

"You should have left it in the ocean," Steve stated seriously, disappearing out the door.

Fury chuckled shaking his head, "Boy, you have no idea how much I wish we had,"

The phone in his pocket began to ring. Not even looking at the caller ID, he flipped it open and placed it to his ear.

"Talk to me,"

"**Sir, its Agent Coulson. We just picked up a hit on the young man we have been tracking for a while now,**"

"What kind of hit?"

"**Major sir, he had to use his powers to save his team and himself from certain death during their latest case and was almost exposed to his team. What do you want to us to do?**"

Fury sighed, pinching the bridge of his nose, "Keep all eyes and ears on him as usual. Don't go and send anyone in, I will do it personally. We could use a man like him on the team,"

"**Team sir? 'The Avengers Initiative'?**"

"Have a plane ready for me and tell Director Vance of the NCIS Headquarters in Quantico that I am on my way," Fury ordered, "Oh and Coulson, I would have to say that Tony Dinozzo would make a fine addition to the Avengers,"

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**PLEASE READ & REVIEW! **

**Thanks to those reviewed last chapter. At this rate I may also go ahead and put this story under the NCIS category as well, just so it may get more people reading it, but this idea is still being considered. **

**I hope you go the whole intense feeling with that, sometimes when I write it, it doesn't feel that way but I would really like to know about you thought it went. ****  
**

**Also, to the guest known as Ryuka - you flaming opinion is noted but ignored as you were extremely rude and I know how bad that story was so I don't need to hear you say it. EXCUSE THE RANT FOR EVERYONE ELSE! **

**Anyhoo, hope you all enjoyed and this will be updated again soon. Though I am still leaning towards a Steve/Tony pairing. **

**JA NE!**


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